BIOGRAPHY - Page 13
Cyclops didn't have much of a break after returning from his recent foray into deep space before the future event Sinister blinded them to arrived: an immensely powerful new mutant signature was detected in a small town in Alaska, the first new mutant since M-Day. By the time the X-Men arrived to investigate it, the town had been razed by both the Purifiers and Mr. Sinister’s Marauders, and the new mutant—in fact a newborn infant—was nowhere in sight. Scott saw this new mutant birth as the last remaining hope for the mutant race. Fearing that Sinister or the Purifiers, who both knew this mutant birth was coming, now possessed the child, the X-Men headed back to their headquarters to regroup. While there, Professor X questioned why Cyclops sent a team into the field without informing him, at which point Cyclops reprimanded Xavier for questioning his leadership. He asked him to stay out of their affairs unless he planned on being useful.
X-Men strike teams learned that it wasn't Sinister or the humans who got to the mutant baby first, but Cable, who was somehow still alive. Cyclops re-formed the long-defunct X-Force with Wolverine in charge and sent them after Cable. When Xavier again questioned his decisions, this time for sending a team of killers after his own son, Cyclops rebuffed his old mentor and demanded he stay out of the way. It turned out, though, that Cyclops didn't need to worry about Cable after all, as he had nothing but the baby's best interests in mind and was just trying to get her to safety.
The time-traveling X-Man he did need to worry about, however, turned out to be none other than Bishop, who placed the blame for his own rotten future solely on the head of this mutant child. These warring factions converged on the Marauders' hideout on Muir Island, where they all battled for control of the baby. Conveniently for the X-Men, Bishop was taken out of the fight by an anti-mutant predator, while Sinister was killed by Mystique, who had been manipulating the events from the beginning in order to cure her daughter Rogue of an otherwise terminal illness. It was in the aftermath of these bloody affairs that Scott reunited with his son, who finally agreed to cede control of the baby’s future to the X-Men. 
As Scott held the little redheaded mutant girl in his arms for the first time, she reached out and touched a locket he wore bearing an image of Jean. In that moment, Cyclops noticed the similarities between this situation and the circumstances that had long ago led him to sending his own son, Nathan Christopher, into the future for safekeeping. He decided to let Cable take care of the baby. However, as Cable departed to the future with the child, Bishop emerged from his unconscious state and fired at them. Although he missed his intended target, he hit—and mortally wounded—Charles Xavier. After taking out Bishop, a mournful Cyclops declared that there were no more X-Men. [Messiah Complex crossover]
With his mentor dead, his team in shambles and the future of the mutant race uncertain, Cyclops decided it was time to change his tactics. No longer would he grant second chances to known traitors, and no longer would mutants sit around passively while waiting for their enemies to come slaughter them. He started by sending Wolverine into the field to eliminate Mystique—permanently. [Wolverine (3rd series) #62-65] 
He ordered X-Force to find Bishop, who escaped in the aftermath of the battle on Muir Island; Cyclops made it clear that dead OR alive was acceptable. Upon learning that Bishop had attacked Forge and stolen his time-travel technology, Scott ordered Beast to start working on building time-travel tech of their own; for the sake of Hank's conscience, he chose to leave the "so we can use it to kill Bishop" part out of it. [Cable (2nd series) #6]
Now that X-Force was operational, Cyclops decided to send his new team of killers to proactively take out the rest of the Purifiers, by any means necessary. X-Force cut, stabbed and murdered its way across the countryside before they got to the Purifiers' current leader, at which point they discovered, to their horror, that the Purifiers had resurrected not only their old enemy Bastion, but an entire rogue's gallery of mutant-hating enemies of the X-Men by using the T/O Virus. [X-Force (3rd series) #1-6]
Because killing their enemies, even in self-defense, had typically gone against the X-Men’s policy, Cyclops kept Wolverine and X-Force's actions secret from all of his peers, including Emma and the rest of the superhero community. When Iron Man confronted him about registering the X-Men according to the SHRA, Cyclops told him he was disbanding the team entirely. The X-Men were technically inactive and regrouping at that point, and since the 198 powered mutants were already registered with O*N*E, Scott defied the need to register again with the SHRA. Cyclops then retreated to the Savage Land with Emma for a much-needed vacation and took some time to himself to think about his recent actions and what the future held for the X-Men. He decided that he was going to do things differently for the X-Men in the future—and that he was going to change how mutants were treated all over the world. [Uncanny X-Men (1st series) #495]
His first task was finding a new base of operations. Luckily, his scout, Angel, found a perfect city to make their new headquarters: San Francisco. 
Unfortunately, it was currently in the thrall of a mutant illusionist who convinced everyone within her vicinity that it was still the height of the Free Love movement of the late 1960's. Cyke and Emma entered the city—which existed in the shadow of the colossal, inert Dreaming Celestial—and made their way to the source of the mass illusion, which they neutralized. In the process of this mission, the X-Men happened to save the life of San Francisco's mayor from a runaway truck. Eternally grateful, the mayor, Sadie Sinclair, welcomed the X-Men into her city with open arms, even promising the city would refuse compliance with the SHRA. [Uncanny X-Men (1st series) #496-499]
Now that he had a new home for the X-Men, Cyclops decided it was time to start gathering his old troops. A tragic incident occurred during his prolonged absence when Donald Pierce tricked a group of young mutants into attacking their elders and ended up killing a former student. This made Cyclops realize he needed to once again create a safe space for young mutants—only this time it would not be a school where they would be defended, but a training institute that would prepare them to defend themselves. Even though he once disagreed with Emma when she proposed this training style, he now believed her way was the right way. [Young X-Men #5-6]
Cyclops established a new high-tech headquarters for the X-Men in the Marin Headlands just outside of San Francisco. While giving Mayor Sinclair a tour of their new home, Greymalkin Industries, she informed him of a tasteless art exhibit opening in town that "celebrated" mutants by using decommissioned Sentinels as artwork. Disgusted, the X-Men attended the exhibit, only to be attacked by a seemingly repowered Magneto, who retreated to the Dreaming Celestial outside the city. Shortly after this commotion, Scott had Emma help him send a telepathic broadcast to all the mutants in the world, inviting them to come seek sanctuary with the X-Men in San Francisco. [Uncanny X-Men (1st series) #500]
Meanwhile, Cyclops continued to blur ethical barriers while working with his Alpha team. He authorized Wolverine to torture and eliminate a fallen opponent, and had Emma lie to Storm about it for him to cover what they were doing. Later, he and Beast opted to vaporize an alternate Earth whose people were on the verge of invading, and destroying, their own. Mutantkind could no longer afford to be cautious and forgiving to their enemies, it seemed. [Astonishing X-Men (3rd series) #25-30]
Later, to Scott's surprise, he discovered Professor X was still alive after all. The terms through which he discovered this, though, did little to rebuild his trust in the man: Xavier telepathically tricked him into leaving the X-Men's base and meeting him in the woods. Scott was still angry at the professor for everything he had done, and it didn’t help that Xavier had recently had an encounter with one of Mr. Sinister's post-mortem fail-safe mechanisms, through which he learned the full extent to which Sinister had manipulated Scott's bloodline. 
When he tried to leave, Xavier refused to let him, which forced Emma to intervene. She conducted some involuntary psychic therapy on Xavier that ended up showing Scott that everything awful Xavier had done, he had done with the best of intentions. However utilitarian his motives, Cyclops came to an understanding with his former mentor and forgave him, at which point Charles officially gave him his blessing to lead the X-Men. [X-Men Legacy (1st series) #215-216]
Cyclops felt increasingly optimistic about the future. He even began building a crib for the messiah baby for her inevitable return, something he never got to do when Nathan was a baby. However, anti-mutant fever still reared its ugly head in their seemingly tolerant city, this time in the form of a Hellfire Club-inspired street gang, who savagely attacked one of Scott’s wards. After torturing one of these "Hellfire Cult" members for information, Cyclops formulated a plan to take them down. He learned that the seeming mastermind behind this gang was the former Hellion Empath but, during their raid of Empath's headquarters, he was telepathically seduced by a woman he thought was Emma—only to discover later that it was not Emma, but the psionic ghost of his dead wife, Madelyne Pryor. [Uncanny X-Men (1st series) #501-503]
Meanwhile, Beast finally figured out the reason Cyclops asked him to build time-travel tech was so he could send X-Force to kill Bishop. When Beast called him on it, Scott evaded the question. [Cable (2nd series) #6]
For a moment, however, it seemed time-travel might not be necessary to find Bishop, as he conveniently reappeared in the present. X-Force managed to apprehend him, allowing Cyclops and Emma to torture him for information about what he was doing. Unsurprisingly, this further alienated Beast from Scott. From this interrogation, Cyclops learned that Bishop was destroying the planet in the future one continent at a time in order to corner Cable and the messiah baby. Shortly after revealing this horrifying bombshell, Bishop set off a trap that allowed him to escape and continue his hunt of Scott’s son. [Cable (2nd series) #7-10]
Scott's questionable actions grew even more questionable when the alien race known as the Skrulls occupied San Francisco as part of their secret invasion. To rid the city of the Skrulls, Cyclops had Beast reformulate the infamous Legacy Virus as a biological weapon that would target their physiology. Despite his moral objections, Beast complied and Scott infected the Skrulls with this modified virus. Although he offered them the cure if they agreed to leave—a cure, by the way, he never asked Hank to develop and wasn't even sure existed—the Skrulls chose to commit suicide rather than admit defeat. Enraged, Beast confronted Scott about manipulating him into participating in biological warfare and genocide. Scott merely patted his irate friend on the back and thanked him for his input. [Secret Invasion: X-Men #1-4]
Even Wolverine began to wonder just how far Scott was going to go with his "take no prisoners" attitude. When it was temporarily necessary for the teen healer Josh Foley to learn about X-Force, Cyclops seriously considering having the youth "dealt with" to protect the secret. Thankfully, Elixir preemptively arranged to have his own memories wiped to avoid compromising the team, but Cyclops still felt the need to clarify to Logan that he hadn’t gone evil or been possessed by something; he was merely adapting to the dark, new territory they inhabited. [X-Force (3rd series) #7]
With all the psychics running around, Cyclops worried about whether it was even possible to keep his secrets secret. To hide them from even the most powerful telepaths, he employed a technique Jean had taught him of locking these secrets in an inaccessible black box within his mind—one not even Emma could open. [Uncanny X-Men (1st series) #504]
Outside, anti-mutant hysteria hadn't subsided. In fact, it grew even worse when Simon Trask of Humanity's Last Stand revealed to the world that the recent massacre in Cooperstown, Alaska, had been mutant-related. Cyclops responded to this increasing wave of anti-mutant sentiment by offering all mutants, both powered and depowered, sanctuary in the X-Men's headquarters. When Mayor Sinclair asked him what he was up to, he revealed to her that he was building an army. [Uncanny X-Men (1st series) #505-507]